tbuckley/cabot-search huggingface dataset:
DDDR-33. TARGETING TGFΒ PATHWAY DEPENDENCIES IN GROUP 3 MEDULLOBLASTOMA
Authors: Zulekha Qadeer, Samantha Westelman, Mackenzie Johnson, Shane Grele, Liam Hendrikse, Michael Taylor, William Weiss
Journal: Neuro-Oncology (2022)

Abstract Medulloblastoma (MB) is one of the most prevalent malignant brain tumors in children, with tremendous cognitive and neuroendocrine disability among survivors. Group 3 (G3) MBs have poor overall survival at &amp;lt; 50%, few recurrent mutations, higher frequency of metastasis, and no targeted therapies. Amplification of MYC (c-myc) and activation of TGFβ signaling are frequent in G3 MB. We hypothesize that the TGFβ pathway and MYC contribute to the intrinsic resistance of G3 MB through deregulation of key genes and pathways. We previously established humanized models for SHH MB by introducing MYCN or PTCH1 deletions into neuroepithelial stem (NES) cells derived from normal human induced pluripotent stem cells (hIPSCs). In this study, we transduced NES cells with TGFb effectors activated in G3 MB (ACVR2A, TGFbR1, TGFb1, TGFb3, and SMAD5) alone and/or in combination with MYC, prioritizing combinations observed in patients. Excitingly, both MYC and TGFβ effectors drove tumor formation in vivo with the combination of TGFβ effectors with MYC leading to more aggressive tumors. We thus describe six new humanized isogenic models for both non-MYC and MYC driven G3 MB. We next found that NES cells expressing MYC with either TGFβR1 or TGFβ1 showed resistance to clinical TGFβR1 inhibitors, compared to cells driven by either TGFβR1 or TGFβ1 alone. To decipher mechanisms of resistance, we integrated CUT &amp; RUN to probe for MYC genomic localization and relevant histone PTMs with RNA-seq analysis of MYC and TGFβ pathway driven NES cells. We discovered a subset of genes upregulated in MYC and TGFb-driven lines that are targets of the histone demethylase KDM2B. We postulate that epigenetic remodeling via MYC and recruitment of other MYC-interacting cofactors culminates in transcriptional changes that lead to aggressive disease. Overall, our studies provide insights on identifying new therapeutic avenues for patients with MYC and TGFβ driven G3 MB.
DDDR-12. THE ROLE OF CASEIN KINASE 1 EPSILON IN TEMOZOLOMIDE SENSITIVITY IN GLIOBLASTOMA STEM CELLS
Authors: Shawna Bilton, Zhi Sheng
Journal: Neuro-Oncology (2022)

Abstract A major hurdle in effectively treating glioblastoma is the resistance to current chemotherapy temozolomide (TMZ), exhibited intrinsically in glioblastoma stem cells (GSCs). GSCs are a population of tumor cells that are self-renewing, highly resilient and capable of forming genetically heterogeneous and difficult-to-treat tumors. Therefore, overcoming TMZ resistance holds significant promise in the treatment of glioblastoma. Casein kinase 1 ε (CK1ε) has been identified as a stem cell factor that is important for GSCs to self-renew. However, whether CK1ε confers TMZ resistance in GSCs remains elusive. METHODS To test the role of CK1ε in the chemoresistance of GSCs, we treated GSC adherent cell lines with TMZ, CK1ε inhibitor IC261, and a combination of TMZ plus IC261. Cell viability was assessed with MTS viability assay or CellTiter-Blue viability assay. RESULTS Cell viability was significantly decreased in GSCs treated with 0.8μM IC261 combined with 100μM TMZ as compared to cells treated with either 0.8μM IC261 or 100μM TMZ alone (p &amp;lt; 0.05). We assessed synergistic drug effects using the Bliss independence model to yield Excess Over Bliss (EOB) scores. EOB &amp;gt; 0% indicates a synergistic effect; EOB = 0% indicates additive effect; and EOB &amp;lt; 0% indicates antagonistic effect. Cells treated with 0.8μM IC261 together with 100μM TMZ yielded EOB of &amp;gt; 0%. CONCLUSIONS Previous work has identified CK1ε as an important stem cell factor in the survival GSCs, but there lacked studies testing the role of CK1ε in TMZ chemoresistance in vitro. We demonstrate synergistic inhibition of cell viability in GSCs treated with CK1ε inhibitor IC261 in combination with TMZ. Based on these results, CK1ε is suggested to play an important role in the chemoresistance of GSCs to TMZ.
DISP-11. GENDER DISPARITY REGARDING WORK-LIFE BALANCE SATISFACTION AMONG GERMAN NEURO-ONCOLOGISTS: A YOUNGNOA SURVEY
Authors: Sied Kebir, Lazaros Lazaridis, Wolfgang Wick, Michael Platten, Ghazaleh Tabatabai, Stephanie Combs, Teresa Schmidt, Sarina Agkatsev, Tobias Blau, Irina Mäurer, Ulf Kahlert, Andre Sagerer, Anne Berberich, Sina Heider, Michael Müther, Raphael Bodensohn, Felix Behling
Journal: Neuro-Oncology (2022)

Abstract PURPOSE Satisfaction with work-life balance (WLB) is an essential factor for persistent motivation of early career researchers. However, WLB satisfaction in the neuro-oncological landscape is not well characterized. We present the results of an interdisciplinary survey focusing on WLB satisfaction among neuro-oncologists in Germany. METHODS The questionnaire was sent to 351 physicians, all of whom were members of the Neuro-oncology Working Group “Neuroonkologische Arbeitsgemeinschaft” (NOA) of the German Cancer Society (Deutsche Krebsgesellschaft, DKG). The participants were asked for personal information, individual motivations, scientific interests, activities, individual workload, and job satisfaction. The questionnaire was accessible from 18 March 2021 to 1 April 2021. RESULTS Ninety-six physicians (36 female, 60 male) participated in this survey. Age, gender and relationship status were significantly different between participants who were satisfied and those not satisfied with their WLB. Female participants were less likely to be satisfied with their WLB than male participants (25% vs 75%, p = 0.005). In a logistic regression model, the finding that female participants were less likely to be satisfied with their WLB than male participants remained statistically significant (odds ratio [OR] 0.32; 95% confidence interval [CI] 0.21–0.84, p = 0.023) after accounting for possible confounding variables such as age (OR 1.06; 95% CI 1.01–1.11, p = 0.025), childlessness (children available vs not available, OR 0.40; 95% CI 0.10–1.35, p = 0.156), and relationship status (unmarried vs single, OR 2.49; 95% CI 0.50–13.98, p = 0.275; married vs single, OR 6.18; 95% CI 1.29–35.46, p = 0.029). CONCLUSIONS This survey demonstrates that WLB satisfaction is significantly decreased among female neuro-oncologists in Germany. It highlights the importance of programs such as “Diversity in Neurooncology” (DivINe), founded by the NOA and aiming to address gender disparities.
IMMU-37. ANTI-CD47 TREATMENT POTENTIATES PHAGOCYTOSIS OF MEDULLOBLASTOMA BY M1 POLARIZED MACROPHAGES FOLLOWING IRRADIATION
Authors: Nicholas Gamboa, Cordell Baker, Osama Youssef, Samuel Cheshier
Journal: Neuro-Oncology (2022)

Abstract Medulloblastoma (MB) is the most common malignant brain tumor of childhood and accounts for 15–20% of all pediatric brain tumors. Despite significant advancements over the last decade in our understanding of the molecular underpinnings of MB, the overall risk of recurrence remains high, prognosis remains poor, and available treatment modalities remain limited for patients with this disease. Accordingly, the area of targeting tumor immune resistance has garnered increasing interest as a potentially safe and effective adjunctive therapy. CD47 is a cell surface protein that acts as a primary “don’t eat me” signal to the innate immune system and has been shown to be crucial in allowing tumor cells to evade phagocytosis by tumor-associated macrophages. Several preclinical studies aimed at blocking this “don’t eat me signal” through the application of a mouse anti-human monoclonal antibody (Ab) to CD47 (anti-CD47) have shown promise in pediatric brain tumor models. Further, chemotherapy and irradiation have been shown to increase the expression of pro-phagocytic signals on the surfaces of tumor cells. The authors examined the use of anti-CD47 Ab on the rates of phagocytosis of MB cells undergoing different single-fraction doses of external beam irradiation in vitro. The use of anti-CD47 Ab in the D425 MB cell line phagocytosis assay significantly increased rates of phagocytosis for 0 Gy (4.1% without vs. 20.3% with anti-CD47 Ab; p &amp;lt; 0.0001), 2 Gy (7.4% without vs. 23.4% with anti-CD47 Ab; p &amp;lt; 0.0001), 5 Gy (11.9% without vs. 27.3% with anti-CD47 Ab; p &amp;lt; 0.0001), 10 Gy (21.7% without vs. 34% with anti-CD47 Ab; p &amp;lt; 0.0001), and 20 Gy treatment groups (27.2% without vs. 43.9% with anti-CD47 Ab; p &amp;lt; 0.0001). A similar pattern of phagocytosis potentiation through use of anti-CD47 Ab with increasing doses of radiation was seen in D458 and D341 MB cell lines.
EPCO-34. INTEGRATIVE DNA METHYLATION ANALYSIS OF PEDIATRIC BRAIN TUMORS REVEALS TUMOR TYPE-SPECIFIC DEVELOPMENTAL TRAJECTORIES AND EPIGENETIC SIGNATURES OF MALIGNANCY
Authors: Meeri Pekkarinen, Kristiina Nordfors, Joonas Uusi-Mäkelä, Ville Kytölä, Minna Rauhala, Henna Urhonen, Sergei Häyrynen, Ebrahim Afyounian, Olli Yli-Harja, Wei Zhang, Pauli Helen, Olli Lohi, Hannu Haapasalo, Joonas Haapasalo, Matti Nykter, Juha Kesseli, Kirsi Granberg
Journal: Neuro-Oncology (2022)

Abstract Understanding oncogenic epigenetic mechanisms in brain tumors is crucial for improved diagnosis and treatment. Recently DNA methylation has proven to be powerful for brain tumor characterization and diagnostic classification. To evaluate tumor type specific features, we compared atypical teratoid/rhabdoid tumors (AT/RTs), medulloblastomas (MBs), and choroid plexus tumors with each other by integrating DNA methylation (507 samples), gene expression (120 samples), and transcription factor (TF) -binding data. Different tumor entities were used to find unique changes affecting each of the entities and further to identify functions driven by these changes. Our results provide insight on how the aberrant DNA methylation induces oncogenesis of AT/RTs. These tumors are known for their aggressiveness and exceptionally low mutation rates. Our results suggest that in AT/RT, elevated DNA methylation masks the binding sites of TFs such as NEUROD1, ASCL1 and MYCN driving neural development. DNA methylation in AT/RTs is also associated with reduced gene expression for specific neural regulators such as NEUROG1 and NEUROD2. For MBs, DNA methylation patterns predict a more advanced differentiation state. In MB, we found masked TF binding sites for TFs such as REST and ZEB1 that normally inhibit neural differentiation. We then wanted to further characterize DNA methylation and compared these tumors to pluripotent stem cells (PSCs) and normal fetal brain samples. As a result, we were able to find two different regulatory programs in AT/RTs: One in which DNA methylation is similar to PSCs and which harbors mostly neural TF binding sites. Second program has AT/RT-specific DNA methylation, and these sites are uniquely associated with polycomb repressive complex 2 members. However, this second program also covers neural TF binding sites and is likely to have relevance in oncogenic regulation.
DDDR-34. RECURRENT RELA FUSION-POSITIVE EPENDYMOMA TREATED WITH VAL-083 UNDER EXPANDED ACCESS: A CASE REPORT
Authors: Carlos Kamiya-Matsuoka, Stephanie Knight, John Langlands, Dennis Brown, Vinay Puduvalli
Journal: Neuro-Oncology (2022)

Abstract Ependymoma is a relatively rare central nervous system tumor accounting for 2-9 % of all neuroepithelial tumors. RELA fusion-positive ependymoma is a subgroup associated with supratentorial location, higher WHO grade and worse prognosis. In addition, there is no standard systemic chemotherapy treatment for adults with recurrent disease. VAL-083 is a bi-functional DNA-targeting agent which rapidly induces inter-strand DNA cross-links at N7-guanine inducing double-strand breaks causing cell death and acts independent of MGMT DNA-repair in high-grade gliomas. We report a 40-year-old male who was initially diagnosed with a right parieto-occipital high-grade glioma, with no somatic mutations including IDH1/2 genes, and with unmethylated MGMT promoter status. He initially underwent gross total resection, followed by chemoradiation with concurrent and adjuvant temozolomide for 12 cycles. Sixteen months later, he developed recurrent disease and had a second resection. Inter- and intragenic fusion analysis of tumor tissue revealed C11orf95-RELA fusion and the diagnosis of RELA fusion-positive ependymoma was established. The patient was not eligible to participate in any clinical trial and received VAL-083 under an expanded access program. He was then treated with VAL-083 (30 mg/m2 for 3 consecutive days every 21 days) and completed 12 cycles during a period of 9 months. No grade 3/4 adverse events such as thrombocytopenia, anemia, neutropenia, or lymphopenia were observed. His liver and renal functions were normal. No dose reduction was required. He also received levetiracetam, alprazolam and prochlorperazine, with no drug interactions. Steroid were not required. He has been under surveillance since completion of systemic treatment with VAL-083 and has remained radiologically stable, with no CSF dissemination, after 12 months. This case highlights that VAL-083 may be a treatment option for recurrent RELA fusion-positive ependymoma refractory to temozolomide-based regimens. Clinicaltrials.gov Identifier: NCT03138629. The treatment plans for this EAP patient were approved by MD Anderson Cancer Center IRB.
EPCO-04. TRANSCRIPTIONAL AND CHROMATIN-ACCESSIBILITY HETEROGENEITY IN IDH-MUTANT GLIOMAS
Authors: Anne-Marie Lyne, François Ducray, Florence Cavalli
Journal: Neuro-Oncology (2022)

Abstract Diffuse gliomas are a common type of adult brain tumour, comprising about 80% of adult malignant brain tumours, and are incurable. IDH-mutant gliomas, oligodendroglioma and astrocytoma, can be treated initially but eventually recur and are generally fatal. In this study, we profiled and analysed 23 frozen samples from primary and recurrent IDH-mutant glioma patients with single nucleus multiome sequencing (RNA- and ATAC-seq). In total we assayed around 70,000 malignant cells as well as 30,000 cells from the tumour microenvironment. Using a matrix factorisation approach, we characterised biological signals in the malignant cells from each sample, thereby identifying known and novel processes which vary within and recur across samples. Trajectory analysis was used to reconstruct the developmental hierarchy in IDH-mutant glioma and to investigate plasticity at different hierarchy levels, highlighting differences and similarities across patients and cancer types. Finally, master regulators, which drive malignant transcriptional programs were identified, using the complimentary and concurrent RNA and chromatin accessibility assays. This study provides a unique opportunity to investigate the transcriptomic and epigenetic heterogeneity present in gliomas, as well as the events leading to the development of more aggressive and treatment-resistant glioma tumours.
DDDR-23. IN SILICO DRUG DISCOVERY REVEALS SUBTYPE-SPECIFIC COMBINATION THERAPIES WITH CASEIN KINASE 2 INHIBITOR CX-4945 IN GLIOBLASTOMA
Authors: Nagi Ayad, Robert Suter, Anna Jermakowicz, Simon Kaeppeli
Journal: Neuro-Oncology (2022)

Abstract The treatment for glioblastoma (GBM) is maximal safe resection, temozolomide chemotherapy, and radiation therapy. However, with a median survival of only 15 months, new therapies are needed. GBM tumors are highly heterogeneous and three tumor subtypes, namely classical, proneural, and mesenchymal, have been identified. On a single cell level, differences are even more granular. Casein kinase 2 (CK2), which regulates invasion and important pathways including Wnt, Shh, and Notch in GBM, may be a promising target in distinct subpopulations. The CK2 inhibitor CX-4945 (silmitasertib) is in clinical trials for several cancers, including medulloblastoma. We employed single-cell RNA sequencing and analyzed bulk RNA sequencing data of PDX tumors (Brain Tumor PDX national resource at the Mayo Clinic). We found that on the tumor level, CX-4945 may preferentially target mesenchymal subtypes, which are the most invasive. On a single-cell level, CX-4945 was predicted to target cells with Astrocyte-like and Mesenchymal-like transcriptional states, which we show to become enriched upon treatment with the pan-aurora kinase inhibitor alisertib. Thus, CX-4945 in combination with a treatment targeting tumor subtypes and cell populations that evade CK2 inhibition may achieve beneficial clinical results. We identified several promising small molecules that could complement CX-4945 treatment based on the predicted reversal of the transcriptional disease gene expression signatures, which are specific for each subtype. Among these drugs are multiple anti-cancer agents that have shown favorable tolerability and brain penetrance in patients and may be effective in combination therapies. In a next step, we will evaluate the predicted combinations with CX-4945 in vitro and in vivo, with a particular focus on how they influence invasion and migration.
IMMU-31. PROTEASOME REARRANGED PEPTIDES ARE A NOVEL SOURCE OF ANTIGENS FOR THE PEPTIDE VACCINE IMMUNOTHERAPY OF GLIOBLASTOMAS
Authors: Mario Fidanza, Puja Gupta, Varun Shanker, Nicollette Wong, Stephen Skirboll, Michael Lim, Albert Wong
Journal: Neuro-Oncology (2022)

Abstract pepVIII, an anticancer vaccine targeting EGFRvIII, has been tested in several trials for glioblastoma including ACT IV. a randomized Phase III trial for newly diagnosed patients. While results from ACT IV were equivocal, available data suggests the elimination of EGFRvIII was not robust. Despite its essential role in antigen presentation, enhancing proteasomal processing is an unexploited strategy for improving vaccines. We examined 20 peptides in silico and experimentally, which showed that a tyrosine substitution (Y6-pepVIII) maximizes proteasome cleavage and survival in a subcutaneous tumor model. In an intracranial glioma model, Y6-pepVIII showed a 62 and 31% improvement in median survival compared to control animals and pepVIII-vaccinated mice. Y6-pepVIII vaccination altered tumor-infiltrating lymphocyte subsets and expression of PD-1 on intratumoral T cells. Combination with anti–PD-1 therapy cured 45% of the Y6-pepVIII–vaccinated mice but was ineffective for pepVIII-treated mice. LC-MS/MS analysis of proteasome-digested pepVIII and Y6-pepVIII revealed that most fragments were similar but more abundant inY6-pepVIII digests and 77% resulted from proteasome-catalyzed peptide splicing (PCPS). We identified 10 peptides that bound human and murine MHC class I. Nine were PCPS products and only one peptide was colinear with EGFRvIII, indicating that PCPS fragments may be a component of MHC class I recognition. Despite not being colinear with EGFRvIII, two of three PCPS products tested were capable of increasing survival when administered independently as vaccines. We hypothesize that the immune response to a vaccine represents the collective contribution from multiple PCPS and linear products. Our work suggests a strategy to increase proteasomal processing of a vaccine that results in an augmented immune response and enhanced survival in mice.
IMMU-33. CCL4 DRIVES GLIOBLASTOMA (GBM) TUMOR MICROENVIRONMENT (TME) REPROGRAMMING AFTER TREATMENT WITH A NOVEL MRNA VACCINE
Authors: Farhad Dastmalchi, Nagheme Thomas, Matt Frain, Ghaidaa Ebrahim, Ginger Moore, Macaulay Tomdio, Hector Mendez-Gomez, Elias Sayour, Vignesh Subramaniam, Thomas Angelini, Duane Mitchell, Maryam Rahman
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Our group has developed a patented vaccine platform that combines an mRNA-nanoparticle with CXCL9 loaded polyethylene glycol (PEG) hydrogel. The HCM vaccine is given SQ and recruits a diverse immune cell population to deliver a large payload of mRNA. The objective of these studies was to evaluate the effects of HCM vaccination on the TME. METHODS C57BL/6 mice underwent intracranial implantation of KR158 or GL261 glioma cells. The HCM vaccine was formulated with total tumor mRNA, DOTAP, CXCL9 and PEG hydrogel created in collaboration with the College of Engineering. Survival studies were analyzed with the Mantel-Cox test. Flow cytometry and ELISA data was analyzed using ANOVA. Graphpad was used for statistical analysis. RESULTS Intracranial tumor bearing mice were treated with SQ or intracranial injection of the HCM vaccine (total tumor mRNA, DOTAP, CXCL9, PEG hydrogel). SQ HCM delivery resulted in significant survival benefit whereas intracranial delivery did not (p = 0.0012). In a separate experiment, tumors and spleens were collected for flow cytometry. A significant increase in antigen specific CD8 T cells was found. Separately, after SQ vaccination, tumors were collected for PCR analysis. Tumors treated with HCM vaccination demonstrated significant upregulation of CCL4 and CXCR6. Intracranial tumor bearing mice were treated with HCM vaccination with or without blockade of CCL4. CCL4 blockade resulted in no survival benefit of the vaccine. CONCLUSION The HCM vaccine results in migration of antigen specific CD8 T cells within the TME and significant increases in CCL4. HCM vaccine efficacy is dependent on CCL4.
IMMU-02. STANDARDIZATION OF THERAPY AND MANUFACTURING USING TUMOR-ASSOCIATED ANTIGEN-STIMULATED AUTOLOGOUS DENDRITIC CELLS CO-CULTURED WITH CYTOKINE-INDUCED KILLER CELLS IN CANCER IMMUNOTHERAPY
Authors: Chun-Ming Yen, Yun-Yen Fu
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND The application of DC-CIK in the field of cancer immunotherapy has been shown to be an effective treatment. However, the cost of DC-CIK treatment is prohibitive for many patients, and the lack of standard manufacturing processes and treatment strategies are the main limitations. METHODS Our experiments used tumor lysate instead of tumor cell line as tumor-associated antigen source with DCs co-culture. We provide the most efficient method for obtaining autologous DC-CIK cells from peripheral blood. Flow cytometry was used to evaluate DCs activation, CBA assay was used to quantify cytokines secreted by CIK cells, and the antitumor activity of DC-CIK was evaluated in vitro by K562 cell line. RESULTS We demonstrate that the manufacturing process of employing frozen Peripheral Blood Mononuclear Cells (PBMCs) can balance patient’s comfort and economic benefits. DC-CIK can effectively upgrade the immunological specificity of CIK cells to tumors in the presence of tumor-associated antigen. In vitro experiments showed that when the number of DC: CIK cells was co-cultured in 1:20 ratio on the 14th day, the amount of cytokine secreted by CIK cells was the largest, and the anti-tumor immune effect was the most potent. When the number of CIK: K562 cells was in 25:1 ratio, the cytotoxic activity of CIK on K562 cells was the highest. CONCLUSION We developed an efficient activated fashion of DC:CIK, established the optimal ratio of DC-CIK immunologic activity and the best cytotoxic model of CIK to K562 cells.